Problem installing from source: no CONTENTS files

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Problem installing from source: no CONTENTS files

MarkBravington
I've just had the error below while trying to install a package from
source under R2.2.1 and Windows XP. I recall encountering this
sporadically in the past. It is a pretty confusing message and took me
quite some time to figure out; I've seen queries about it on the R site
search, but couldn't find a reply. There's an attempted diagnosis and
suggested cure below.

D:\r2.0\debug>rcmd INSTALL --library=d:/rpackages/r2.2.1 --docs=normal
debug

---------- Making package debug ------------
<<snipped>>
installing indices
cat: C:/R/RW2021/library/*/CONTENTS: No such file or directory

What I think is happening is this. Because I installed R from binary
*without* HTML help, no CONTENTS files are created for the packages.
When running RCMD INSTALL, this causes an error in the MakePkg file (in
src/gnuwin32 on my machine), in the "indices" section at the line
starting @$(CAT) below. Commenting out the CAT line seems to work fine,
in that installation proceeds OK, and regular non-HTML help and
help.search are available for the package. The comment two lines up
suggests that the behaviour is a bug; maybe a TRY-style wrapper could be
used? If not, a different error message would be handy. I don't
understand enough about makefiles to suggest a patch, unfortunately.

indices:
        @$(ECHO) "  installing indices"
        @$(ECHO) "invisible(.libPaths(c(.Library,\"$(RLIB)\",
.libPaths()))); tools:::.install_package_indices('.', '"$(DPKG)"')" | \
          R_DEFAULT_PACKAGES=NULL LC_COLLATE=C R_OSTYPE=windows $(REXE)
> /dev/null
# need not have HTML installed when building packages
        @$(MKDIR) -p $(RHOME)/doc/html/search
        @$(CAT) $(RHOME)/library/*/CONTENTS >
$(RHOME)/doc/html/search/index.txt


Mark Bravington
CSIRO Mathematical & Information Sciences
Marine Laboratory
Castray Esplanade
Hobart 7001
TAS

ph (+61) 3 6232 5118
fax (+61) 3 6232 5012
mob (+61) 438 315 623

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Re: Problem installing from source: no CONTENTS files

Prof Brian Ripley
This will only happen if you installed R without HTML help and then
install a package *with* HTML help *and* do so into a non-standard
directory.  That seems an arcane thing to do: why do you want HTML help
for some packages and not others?  You will end up with a partially
functional system.

The fix is simple: put '-' at the beginning of that line (after the tab)
in MakePkg.  I've put a more complete solution in R-devel.

On Mon, 9 Jan 2006 [hidden email] wrote:

> I've just had the error below while trying to install a package from
> source under R2.2.1 and Windows XP. I recall encountering this
> sporadically in the past. It is a pretty confusing message and took me
> quite some time to figure out; I've seen queries about it on the R site
> search, but couldn't find a reply.

I don't believe those are the same thing.

> There's an attempted diagnosis and
> suggested cure below.
>
> D:\r2.0\debug>rcmd INSTALL --library=d:/rpackages/r2.2.1 --docs=normal
> debug
>
> ---------- Making package debug ------------
> <<snipped>>
> installing indices
> cat: C:/R/RW2021/library/*/CONTENTS: No such file or directory
>
> What I think is happening is this. Because I installed R from binary
> *without* HTML help, no CONTENTS files are created for the packages.
> When running RCMD INSTALL, this causes an error in the MakePkg file (in
> src/gnuwin32 on my machine), in the "indices" section at the line
> starting @$(CAT) below. Commenting out the CAT line seems to work fine,
> in that installation proceeds OK, and regular non-HTML help and
> help.search are available for the package. The comment two lines up
> suggests that the behaviour is a bug; maybe a TRY-style wrapper could be
> used? If not, a different error message would be handy.

The error message is completely informative: why would you want to change
it?

> I don't understand enough about makefiles to suggest a patch,
> unfortunately.

A good learning project for you?


>
> indices:
> @$(ECHO) "  installing indices"
> @$(ECHO) "invisible(.libPaths(c(.Library,\"$(RLIB)\",
> .libPaths()))); tools:::.install_package_indices('.', '"$(DPKG)"')" | \
>  R_DEFAULT_PACKAGES=NULL LC_COLLATE=C R_OSTYPE=windows $(REXE)
>> /dev/null
> # need not have HTML installed when building packages
> @$(MKDIR) -p $(RHOME)/doc/html/search
> @$(CAT) $(RHOME)/library/*/CONTENTS >
> $(RHOME)/doc/html/search/index.txt
>
>
> Mark Bravington
> CSIRO Mathematical & Information Sciences
> Marine Laboratory
> Castray Esplanade
> Hobart 7001
> TAS
>
> ph (+61) 3 6232 5118
> fax (+61) 3 6232 5012
> mob (+61) 438 315 623
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Problem installing from source: no CONTENTS files

MarkBravington
In reply to this post by MarkBravington
> Brian D. Ripley,                  [hidden email]

> This will only happen if you installed R without HTML help
> and then install a package *with* HTML help *and* do so into
> a non-standard directory.  That seems an arcane thing to do:
> why do you want HTML help for some packages and not others?  
> You will end up with a partially functional system.
>
> The fix is simple: put '-' at the beginning of that line
> (after the tab) in MakePkg.  I've put a more complete
> solution in R-devel.

Thanks for the fix. I think the message is more general, though. What I
want to do is install the package just with "vanilla help"-- the stuff
that comes up in the pager. According to "RCMD INSTALL --help" the only
options are "doc=none/normal/chtml/all"-- there's no "vanilla" or
equivalent. If I do "doc=none" I don't get vanilla help. So "doc=normal"
is required, and this tries to do HTML which I don't need. A
vanilla-only option would be ideal, I guess.

>
> On Mon, 9 Jan 2006 [hidden email] wrote:
>
> > I've just had the error below while trying to install a
> package from
> > source under R2.2.1 and Windows XP. I recall encountering this
> > sporadically in the past. It is a pretty confusing message
> and took me
> > quite some time to figure out; I've seen queries about it on the R

<<snipped>>

> > ---------- Making package debug ------------ <<snipped>> installing
> > indices
> > cat: C:/R/RW2021/library/*/CONTENTS: No such file or directory

<<snipped>>

> > be used? If not, a different error message would be handy.
>
> The error message is completely informative: why would you
> want to change it?

I should have said "an additional error message" instead of "a
different...". It's pretty difficult for a user to track down where &
why it is occurring and whether it matters-- accurate, yes, but not
informative! Anyway, maybe otiose now (the more complete solution hasn't
made it to the R-devel I got this morning, so I can't check yet).

>
> > I don't understand enough about makefiles to suggest a patch,
> > unfortunately.
>
> A good learning project for you?

true no doubt-- but just one out of so many ... :(

Thanks
Mark

> >
> > Mark Bravington
> > CSIRO Mathematical & Information Sciences Marine Laboratory Castray
> > Esplanade Hobart 7001 TAS
> >
> > ph (+61) 3 6232 5118
> > fax (+61) 3 6232 5012
> > mob (+61) 438 315 623
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
> --
> Brian D. Ripley,                  [hidden email]
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
>
>

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